1VPK

Crystal structure of DNA polymerase III, beta subunit (TM0262) from Thermotoga maritima at 2.00 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP42936.25% PEG-6000, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7354.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.702α = 90
b = 91.702β = 90
c = 111.463γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2003-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
125099.780.05839.8210.663263946.77
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.650.8092.258.583172

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JQJ247.6330962165699.620.198140.196320.23207RANDOM46.909
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.110.11-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.794
r_dihedral_angle_4_deg17.97
r_dihedral_angle_3_deg14.727
r_dihedral_angle_1_deg6.838
r_scangle_it4.348
r_scbond_it2.739
r_angle_refined_deg1.668
r_mcangle_it1.649
r_mcbond_it1.174
r_angle_other_deg0.835
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.794
r_dihedral_angle_4_deg17.97
r_dihedral_angle_3_deg14.727
r_dihedral_angle_1_deg6.838
r_scangle_it4.348
r_scbond_it2.739
r_angle_refined_deg1.668
r_mcangle_it1.649
r_mcbond_it1.174
r_angle_other_deg0.835
r_mcbond_other0.267
r_symmetry_vdw_refined0.25
r_nbd_refined0.206
r_symmetry_vdw_other0.196
r_xyhbond_nbd_refined0.184
r_nbd_other0.177
r_nbtor_refined0.173
r_symmetry_hbond_refined0.124
r_chiral_restr0.106
r_nbtor_other0.087
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2853
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement